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ghm17 / LOGODetect

LOGODetect is a powerful tool to identify small segments that harbor local genetic correlation between two traits/diseases.
GNU General Public License v3.0
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C1L2 column = 0 #22

Closed gina-parcesepe closed 2 months ago

gina-parcesepe commented 1 year ago

For the "summary of LD scores in /Results/tmp-files/S-LDSC/LOGODetect_theta_0.5_chr1.l2.ldscore.gz" I'm having a column of zeros under the "C1L2".

This is happening for all chromosomes, is there an obvious reason this could be?

LOGODetect issue
ghm17 commented 1 year ago

The reason might be that LOGODetect identify no significant regions for theta=0.5. There were some minor updates for the script a few days ago. Please use the updated tool which skips the step calculating stratified genetic covariance if no region is identified for a given theta.

gina-parcesepe commented 1 year ago

This happens for all chromosomes and all theta, but from previous analyses I know that there are regions of correlation. I'll try re-run with the updated code.